New candidates for regulated gene integrity revealed through precise mapping of integrative genetic elements

φSa3mw Prophage as a Molecular Regulatory Switch of Staphylococcus aureus β-toxin Production

(2019) Phuong M. Tran et al.   JOURNAL OF BACTERIOLOGY

Cryptic inoviruses revealed as pervasive in bacteria and archaea across Earth’s biomes

(2019) Simon Roux et al.   Nature Microbiology

Improved genomic island predictions with IslandPath-DIMOB

(2018) Claire Bertelli et al.   BIOINFORMATICS

Microbial genomic island discovery, visualization and analysis

(2018) Claire Bertelli et al.   BRIEFINGS IN BIOINFORMATICS

Mobile DNAs as Ecologically and Evolutionarily Independent Units of Life

(2018) Timothy M. Ghaly et al.   TRENDS IN MICROBIOLOGY

ICEberg 2.0: an updated database of bacterial integrative and conjugative elements

(2018) Meng Liu et al.   NUCLEIC ACIDS RESEARCH

The Pfam protein families database in 2019

(2018) Sara El-Gebali et al.   NUCLEIC ACIDS RESEARCH

High throughput ANI analysis of 90K prokaryotic genomes reveals clear species boundaries

(2018) Chirag Jain et al.   Nature Communications

Control of Recombination Directionality by the Listeria Phage A118 Protein Gp44 and the Coiled-Coil Motif of Its Serine Integrase

(2017) Sridhar Mandali et al.   JOURNAL OF BACTERIOLOGY

Mechanism of bacterial gene rearrangement: SprA-catalyzed precise DNA recombination and its directionality control by SprB ensure the gene rearrangement and stable expression of spsM during sporulation in Bacillus subtilis

(2017) Kimihiro Abe et al.   NUCLEIC ACIDS RESEARCH

IslandViewer 4: expanded prediction of genomic islands for larger-scale datasets

(2017) Claire Bertelli et al.   NUCLEIC ACIDS RESEARCH

A novel non prophage(-like) gene-intervening element within gerE that is reconstituted during sporulation in Bacillus cereus ATCC10987

(2017) Kimihiro Abe et al.   Scientific Reports

A highly specific phage defense system is a conserved feature of the Vibrio cholerae mobilome

(2017) Brendan J. O’Hara et al.   PLoS Genetics

Pneumococcal prophages are diverse, but not without structure or history

(2017) Angela B. Brueggemann et al.   Scientific Reports

Identification and analysis of integrons and cassette arrays in bacterial genomes

(2016) Jean Cury et al.   NUCLEIC ACIDS RESEARCH

GI-SVM: A sensitive method for predicting genomic islands based on unannotated sequence of a single genome

(2016) Bingxin Lu et al.   Journal of Bioinformatics and Computational Biology

A Novel Method to Predict Genomic Islands Based on Mean Shift Clustering Algorithm

(2016) Daniel M. de Brito et al.   PLoS One

A new perspective on lysogeny: prophages as active regulatory switches of bacteria

(2015) Ron Feiner et al.   NATURE REVIEWS MICROBIOLOGY

Prokka: rapid prokaryotic genome annotation

(2014) T. Seemann   BIOINFORMATICS

Islander: a database of precisely mapped genomic islands in tRNA and tmRNA genes

(2014) Corey M. Hudson et al.   NUCLEIC ACIDS RESEARCH

SigHunt: horizontal gene transfer finder optimized for eukaryotic genomes

(2013) K. S. Jaron et al.   BIOINFORMATICS

A proposed mechanism for IS607-family serine transposases

(2013) Martin R Boocock et al.   Mobile DNA

TnpPred: A Web Service for the Robust Prediction of Prokaryotic Transposases

(2012) Gonzalo Riadi et al.   COMPARATIVE AND FUNCTIONAL GENOMICS

Evolution and variation of the nifD and hupL elements in the heterocystous cyanobacteria

(2011) B. J. Henson et al.   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

Resolvase-like serine recombinase mediates integration/excision in the bacteriophage ϕRSM

(2010) Ahmed Askora et al.   JOURNAL OF BIOSCIENCE AND BIOENGINEERING

INDeGenIUS, a new method for high-throughput identification of specialized functional islands in completely sequenced organisms

(2010) Sakshi Shrivastava et al.   JOURNAL OF BIOSCIENCES

Detecting genomic islands using bioinformatics approaches

(2010) Morgan G. I. Langille et al.   NATURE REVIEWS MICROBIOLOGY

FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments

(2010) Morgan N. Price et al.   PLoS One

Variations on the tmRNA gene

(2010) Chunhong Mao et al.   RNA Biology

Challenging a Paradigm: the Role of DNA Homology in Tyrosine Recombinase Reactions

(2009) L. Rajeev et al.   MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS

Detection of genomic islands via segmental genome heterogeneity

(2009) Aaron J. Arvey et al.   NUCLEIC ACIDS RESEARCH

Evaluation of genomic island predictors using a comparative genomics approach

(2008) Morgan GI Langille et al.   BMC BIOINFORMATICS

Phage-Associated Mutator Phenotype in Group A Streptococcus

(2008) J. Scott et al.   JOURNAL OF BACTERIOLOGY